I'm analyzing the microbal communities of some marine sponges, and would like to highlight which OTUs are shared between groups of samples... I'd also like to see exactly what are those OTUs (not just the number of shared OTUs).
Regards
Danilo
A venn diagram is basically a list of all shared OTUs between each and all of your samples. To do that, what ever script you use first generates said list than counts the numbers and plot the circles.
There are numerous ways you can do that:
A) The qiime way, just use whatever python script they got in their arsenal, I'm guessing it's this one...
http://qiime.org/scripts/shared_phylotypes.html
B) The mother way, transform your qiime otu table in to a mother shared file (http://www.mothur.org/wiki/Shared_file) and then use the venn command (http://www.mothur.org/wiki/Venn)
C) The R way, import your qiime OTU table to R and use the Venn package to generate the Venn diegram (you will have to output the list on shared OTU from the R list object) alternatively you can use the script compiled by the guys from Hallam's lab to do that (they also give a very basic R tutorial)
https://github.com/hallamlab/mp_tutorial/wiki/Introduction-to-Downstream-Analysis-in-R
D) The hard way, import the OTU table to excel and use the countif command with all the conditions you require (i.e pairwise and multiple comparisons), than filter your results accordingly.
Ido
Thank you very much! Ido and Mathew.
Venny is very nice!
I did using the Excel tool. Because i needed to know those OTUs and abundance relative for my dataset. After, I took to Venny.
Regards
Danilo
Hi Danilo,
When you use the tool suggested by Mathew A Beale, in addition that it gives you the number of the shared OTUs but if you click on the number it will show you which OTUs are shared
Good luck
Ahmed
Another nice online tool which works the same way as Venny, but it also allows you to upload files:
http://bioinformatics.psb.ugent.be/webtools/Venn/
https://probes.pw.usda.gov/MetaCoMET/MetaCoMET_pending.php?ID=c8b73d4dbd5a9af300b1a856c79d0b7f
Check following link for:
- 3-lists Venn diagrams – VIB
- 4-lists Venn diagrams – Venny 2.0
https://bioinfo2.ugr.es/ceUGR/venn-diagram/
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